Learn to use the mixer in your church. Although most of them look the same, each mixer has different design nuances. Read the manual, which will explain the functions of certain buttons, sliders and knobs. Manuals often include tips on when (and to what extent) you should incorporate a certain feature.
A stereo system sends different signals to the left and right speakers, often creating a richer depth and feel to music. However, stereo signals are not suited for a church where people sit at various distances from the speakers. An audience that should hear both left and right speakers equally will find it unpleasant to sit off-center. Use a mono system (leaving the "Pan" knob on all channels in the center) for a simpler and more effective audio experience for the overall congregation.
Every church sound system uses microphones. Dynamic microphones pick up sound a small distance away. Condenser microphones pick up sound in a large area. Learn what types of microphones (and in what orientation) to use in different situations. General suggestions include: dynamic microphones for personal vocals, individual drums and guitar amplifiers; condenser microphones for choirs and drum set overheads.
Gain knobs and volume faders serve different purposes. Set the gain for each channel so that the loudest your musician plays or sings still sends through a clear, undistorted sound. Use the volume faders to set the overall mix of the band. Make sure you can hear the vocals, but do not let them overpower the instruments. Adjust the overall volume carefully, so it does not damage the congregation's ears. Lower volumes also allow the congregation to hear their own voices, which can establish a sense of community.
If the sound system has monitoring (speakers pointed toward the stage so musicians can hear themselves), take advantage of this feature. Musicians who can hear themselves will feel more confident and play better. Many sound systems use an auxiliary send for monitoring, but each sound system can set up monitoring differently, so learn how to run your particular system.
Once you are confident with the basics, continue to learn how to improve the sound of your system. More advanced sound techniques include equalization, room acoustics/feedback suppression and stage noise.